Variant report

Variant	rs2279743
Chromosome Location	chr12:57377509-57377510
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:57144393..57147298-chr12:57377477..57379944,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000198056	Chromatin interaction
ENSG00000025423	Chromatin interaction

Extended variants
information (count: 128 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:109)

rs_ID	r²[population]
rs10400412	0.95[ASN][1000 genomes]
rs10400555	0.95[ASN][1000 genomes]
rs1044939	0.90[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs10506350	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs10506351	0.90[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs1072670	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs11832487	0.96[ASN][1000 genomes]
rs11834851	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs11834856	0.87[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs11836517	0.99[ASN][1000 genomes]
rs12099695	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs12810024	0.90[CHB][hapmap];0.92[CHD][hapmap];0.86[JPT][hapmap];0.95[ASN][1000 genomes]
rs12810837	0.97[ASN][1000 genomes]
rs12812499	0.84[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs12815538	0.80[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs12818342	0.87[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs12824682	0.87[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs12827039	0.86[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs12827286	0.84[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs1552245	0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs17119301	1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs17119327	0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs17119330	0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs17119344	0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs17119352	0.90[ASN][1000 genomes]
rs17119386	0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs17119388	0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs17119390	0.90[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs17119407	0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs17119416	1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs17119418	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs1843311	0.84[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs1843312	0.84[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs1843313	0.84[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs2035545	0.86[JPT][hapmap]
rs2167306	0.86[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs2270736	0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs2270737	0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs2270739	0.93[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2279373	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs2291855	0.90[CHB][hapmap];0.86[JPT][hapmap];0.95[ASN][1000 genomes]
rs2371717	0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs28589663	0.99[ASN][1000 genomes]
rs2888139	0.84[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs3024974	0.92[CHD][hapmap]
rs34186462	0.87[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs34253098	0.82[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs34359134	0.86[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs34762603	0.82[ASN][1000 genomes]
rs34969650	0.87[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs35034299	0.86[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs35243318	0.86[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs35493121	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs3782329	0.90[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs3782330	0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs3803018	0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs3894415	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4016338	0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs4039	0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs4143085	0.90[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs56128678	0.90[ASN][1000 genomes]
rs56270558	0.90[ASN][1000 genomes]
rs56354404	0.90[ASN][1000 genomes]
rs57056392	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs57129030	0.87[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs57351760	0.97[ASN][1000 genomes]
rs57558853	0.95[ASN][1000 genomes]
rs58298943	0.97[ASN][1000 genomes]
rs58389529	0.90[ASN][1000 genomes]
rs60258120	0.82[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs60273384	0.99[ASN][1000 genomes]
rs60380217	0.86[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs61504157	0.91[ASN][1000 genomes]
rs67476535	0.99[ASN][1000 genomes]
rs67771054	0.80[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs67844278	0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs68126184	0.97[ASN][1000 genomes]
rs697222	0.81[CHD][hapmap];0.85[JPT][hapmap];0.81[ASN][1000 genomes]
rs7135297	0.82[ASN][1000 genomes]
rs7136770	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs71461303	0.97[ASN][1000 genomes]
rs72482268	1.00[ASN][1000 genomes]
rs7298475	1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs73114426	0.95[ASN][1000 genomes]
rs73114428	0.95[ASN][1000 genomes]
rs73114434	0.95[ASN][1000 genomes]
rs73114436	0.95[ASN][1000 genomes]
rs73114437	0.93[ASN][1000 genomes]
rs73114446	0.90[ASN][1000 genomes]
rs73114452	0.90[ASN][1000 genomes]
rs73114457	0.90[ASN][1000 genomes]
rs73114459	0.90[ASN][1000 genomes]
rs73114467	0.90[ASN][1000 genomes]
rs73114468	0.90[ASN][1000 genomes]
rs73114472	0.88[ASN][1000 genomes]
rs73116494	0.82[ASN][1000 genomes]
rs73116501	0.82[ASN][1000 genomes]
rs73131120	0.97[ASN][1000 genomes]
rs733629	0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs746049	1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs7487948	0.87[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs754398	0.96[ASN][1000 genomes]
rs755221	0.90[ASN][1000 genomes]
rs7956166	0.87[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs7961920	0.93[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.84[TSI][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7962771	1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs7969312	0.87[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs7972615	0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs901068	1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:19 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1040850	chr12:57055011-57679209	Strong transcription Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	181 gene(s)	inside rSNPs	diseases
2	nsv1043846	chr12:57323709-57377509	Weak transcription Flanking Bivalent TSS/Enh Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
3	nsv428590	chr12:57329214-57527358	Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Weak transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
4	esv12940	chr12:57331182-57379580	Weak transcription Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
5	nsv1051116	chr12:57331370-57380365	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
6	nsv559019	chr12:57331741-57377509	Flanking Active TSS Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
7	nsv899108	chr12:57331741-57377509	Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
8	nsv899109	chr12:57331741-57381259	Enhancers Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	13 gene(s)	inside rSNPs	diseases
9	nsv436148	chr12:57331980-57377764	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
10	esv3394817	chr12:57334133-57378642	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
11	nsv512276	chr12:57334563-57379261	Enhancers Weak transcription Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
12	esv3387082	chr12:57334915-57379407	Enhancers Strong transcription Weak transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
13	esv2760274	chr12:57335481-57377509	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
14	esv2761077	chr12:57335481-57377509	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
15	nsv973962	chr12:57335927-57377803	Weak transcription Bivalent Enhancer Enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
16	nsv559021	chr12:57338716-57381259	Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region	13 gene(s)	inside rSNPs	diseases
17	nsv832428	chr12:57340609-57535694	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
18	nsv516039	chr12:57342188-57377509	Genic enhancers Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
19	esv15919	chr12:57374348-57379880	Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats	Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2279743	STAT6	cis	multi-tissue	Pritchard

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:57361800-57389000	Weak transcription	Aorta	Aorta
2	chr12:57370800-57379800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
3	chr12:57370800-57381200	Weak transcription	Brain Anterior Caudate	brain
4	chr12:57371600-57381000	Weak transcription	Brain Inferior Temporal Lobe	brain
5	chr12:57372000-57384800	Weak transcription	Gastric	stomach
6	chr12:57372200-57384800	Weak transcription	Primary T cells from cord blood	blood
7	chr12:57372600-57381000	Weak transcription	Spleen	Spleen
8	chr12:57372800-57381000	Weak transcription	Stomach Smooth Muscle	stomach
9	chr12:57373200-57388600	Weak transcription	Fetal Brain Female	brain
10	chr12:57373200-57388800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr12:57374400-57379600	Weak transcription	HMEC	breast
12	chr12:57374400-57379800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr12:57374600-57379200	Weak transcription	NHEK	skin
14	chr12:57374600-57379800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr12:57374600-57379800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr12:57375200-57381600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr12:57375600-57379800	Weak transcription	Placenta Amnion	Placenta Amnion
18	chr12:57377000-57381000	Weak transcription	Brain Hippocampus Middle	brain
19	chr12:57377000-57395200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood

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